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- PDB-5vii: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -

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Basic information

Entry
Database: PDB / ID: 5vii
TitleCrystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-fluoropropyl)phenyl-ACEPC
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / sleep / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / locomotion / regulation of monoatomic cation transmembrane transport / response to morphine / cellular response to lipid / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / regulation of NMDA receptor activity / protein heterotetramerization / glutamate binding / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of axonogenesis / spinal cord development / dopamine metabolic process / suckling behavior / startle response / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / response to amine / modulation of excitatory postsynaptic potential / response to lithium ion / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of protein targeting to membrane / regulation of postsynaptic membrane potential / phosphatase binding / glutamate receptor binding / postsynaptic density, intracellular component / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / multicellular organismal response to stress / long-term memory / monoatomic cation channel activity / regulation of neuron apoptotic process / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse
Similarity search - Function
: / : / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel ...: / : / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5DY / GLYCINE / DI(HYDROXYETHYL)ETHER / Glutamate receptor / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsMou, T.-C. / Conti, P. / Pinto, A. / Tamborini, L. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Authors: Lind, G.E. / Mou, T.C. / Tamborini, L. / Pomper, M.G. / De Micheli, C. / Conti, P. / Pinto, A. / Hansen, K.B.
History
DepositionApr 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
SupersessionMay 17, 2017ID: 5DDX
Revision 1.1May 17, 2017Group: Other
Revision 1.2Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7646
Polymers65,1252
Non-polymers6394
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint6 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.582, 87.362, 122.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31785.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959, UniProt: G3V9C5

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Non-polymers , 5 types, 426 molecules

#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-5DY / 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid


Mass: 335.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18FN3O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS SAMPLE SEQUENCE MATCHES WITH NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonia Acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.951→20.01 Å / Num. obs: 42271 / % possible obs: 97.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.59
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 3721 / Rsym value: 0.476 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NF8

4nf8


Resolution: 1.951→20.006 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2000 4.73 %
Rwork0.1998 --
obs0.2027 42261 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→20.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 44 422 4813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084481
X-RAY DIFFRACTIONf_angle_d0.8946043
X-RAY DIFFRACTIONf_dihedral_angle_d11.1672673
X-RAY DIFFRACTIONf_chiral_restr0.054666
X-RAY DIFFRACTIONf_plane_restr0.006769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9512-20.38781220.3532466X-RAY DIFFRACTION85
2-2.0540.32651350.31712700X-RAY DIFFRACTION94
2.054-2.11440.34111380.28792777X-RAY DIFFRACTION95
2.1144-2.18250.32521420.26332870X-RAY DIFFRACTION97
2.1825-2.26040.31811410.2532844X-RAY DIFFRACTION98
2.2604-2.35080.31971440.22872886X-RAY DIFFRACTION99
2.3508-2.45760.30451440.21342893X-RAY DIFFRACTION99
2.4576-2.58690.33811440.21362907X-RAY DIFFRACTION99
2.5869-2.74860.26671450.2022911X-RAY DIFFRACTION99
2.7486-2.96020.24911450.19462934X-RAY DIFFRACTION99
2.9602-3.2570.26251470.19332952X-RAY DIFFRACTION100
3.257-3.72560.22071480.17012978X-RAY DIFFRACTION100
3.7256-4.68390.18521490.14832999X-RAY DIFFRACTION100
4.6839-20.00660.23761560.17063144X-RAY DIFFRACTION100

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